PCIe is much better in a new system simply because AGP is nearly dead. PCIe x16 slots are the replacement for AGP slots for vid cards. So in terms of upgrading potential, PCIe is infinitely better. New AGP vid cards are dying and all the latest vid cards are PCIe.
That's not to say that all PCIe vid cards are better than AGP vid cards, though. PCIe and AGP are merely the expansion slots. Which vid card you put in the slot is going to determine its gaming performance. Vid cards are not all created equally by any stretch of the imagination. Check the website link in my sig - my friend and I made that website, and it's chock-full of tech specs of all kinds.